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The emerging paradigm is that TEs may be considered as templates of pre-organized combinations of binding sequences which can then move around in the genome carrying an already prepackaged combinatorial regulatory information which can subsequently be fine tuned by local evolutionary moves (mainly point mutations) according to the specific needs of the target genes.
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Furthermore, we may identify the binding regions on the soybean DNA sequences, which can further help biologists target the regulated regions on soybean genome.
From an extensive analysis of protein-DNA complexes, we identified powerful features of DNA and protein sequences which can be used in predicting protein binding sites in DNA sequences.
We have also calculated GC content of both piRNA clusters and piRNA sequences which can provide an overview on the target binding stability of the piRNAs.
But then you have these set pieces, these sequences, which can drop in kind of anywhere.
These molecules often contain adhesion-binding sequences, which may potentially be replaced by synthetic peptides.
Tbx proteins are sequence-specific DNA binding proteins which can serve as transcriptional repressors or activators (Wardle and Papaioannou, 2008).
With the DNA cleavage action itself showing no sequence preference, the specificity of ZFN and TALEN is determined by their DNA-binding domains, which can be engineered to recognize specific sequence in the gene of interest.
They consist of a central DNA-binding domain that directs the receptor to specific DNA sequences within a gene promoter, and a ligand-binding domain, which can accommodate a variety of different compounds.
Through a very thorough sequence/structure analysis, authors built a PKA-specific binding motif model, which can discriminate between PKA phosphorylation sites and other potential serine/threonine sites.
Motifs correspond to short sequences (6 10 bp), often recognized by a DNA-binding protein, and which can be represented by a consensus sequence.
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